Download genome

Downloads genome DNA, cDNA, annotation, and a reusable annotation database.

Step type:

Core step

Run this step

ASOkai run --step download-genome --config-file ./config.yaml

Example configuration for this step:

datadir: ./data
parameters:
  genome:
    assembly: GRCh38
    release: 114
    source: ensembl
    species: Homo_sapiens

Parameters

These scalar configuration values are passed to this step.

Configuration path	Details
parameters.genome.assembly	Accepted value: string; minimum string length: 1 Requirement: Required Description: Genome assembly ID, such as GRCh38.
parameters.genome.release	Accepted value: integer; minimum: 1 Requirement: Required Description: Genome data release number (currently Ensembl).
parameters.genome.source	Accepted value: string Requirement: Default and only value: ensembl Description: Genome data source.
parameters.genome.species	Accepted value: string; minimum string length: 1 Requirement: Required Description: Ensembl species name, such as Homo_sapiens.

Inputs

This step has no file inputs or producer dependencies.

Resources

Configurable resources use the first value in the resolution order shown below.

Resource setting	Details
memory_mb	Step override: resources.download-genome.memory_mb Shared default: resources.default.memory_mb Built-in fallback: 4096 Accepted value: integer; minimum: 1 Description: Memory in mebibytes allocated to this step.

Outputs

File output paths are relative to datadir. Braced names are replaced with the corresponding parameter values.

File outputs

File output	Details
dna	Format: gzip-compressed FASTA reference Description: Primary assembly DNA FASTA. Path template: {assembly}/{source}/{release}/genome/{species}.{assembly}.dna.primary_assembly.fa.gz Example path: GRCh38/ensembl/114/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
cdna	Format: gzip-compressed FASTA reference Description: All-transcript cDNA FASTA. Path template: {assembly}/{source}/{release}/genome/{species}.{assembly}.cdna.all.fa.gz Example path: GRCh38/ensembl/114/genome/Homo_sapiens.GRCh38.cdna.all.fa.gz
annotation	Format: gzip-compressed GTF Description: Gene annotation GTF. Path template: {assembly}/{source}/{release}/genome/{species}.{assembly}.{release}.gtf.gz Example path: GRCh38/ensembl/114/genome/Homo_sapiens.GRCh38.114.gtf.gz
db	Format: SQLite gffutils database Description: Reusable annotation database built by gffutils. Path template: {assembly}/{source}/{release}/genome/{species}.{assembly}.{release}.gtf.db Example path: GRCh38/ensembl/114/genome/Homo_sapiens.GRCh38.114.gtf.db